3URF

Human RANKL/OPG complex

• PDB DOI: https://doi.org/10.2210/pdb3URF/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-11-22 Released: 2012-07-11 
• Deposition Author(s): Wang, X.Q., Luan, X.D., Lu, Q.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.251 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.38 kDa 
• Atom Count: 2,604 
• Modelled Residue Count: 320 
• Deposited Residue Count: 333 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 11, soluble form	A	162	Homo sapiens	Mutation(s): 0  Gene Names: TNFSF11, OPGL, RANKL, TRANCE
UniProt & NIH Common Fund Data Resources
Find proteins for O14788 (Homo sapiens) Explore O14788  Go to UniProtKB:  O14788
PHAROS:  O14788 GTEx:  ENSG00000120659

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 11B	B [auth Z]	171	Homo sapiens	Mutation(s): 0  Gene Names: TNFRSF11B, OCIF, OPG
UniProt & NIH Common Fund Data Resources
Find proteins for O00300 (Homo sapiens) Explore O00300  Go to UniProtKB:  O00300
PHAROS:  O00300 GTEx:  ENSG00000164761

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth Z]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.251 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.8	α = 90
b = 144.8	β = 90
c = 144.8	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Wang, X.Q., Luan, X.D., Lu, Q.Y.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary